Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Molecular Mechanism of pH-Induced Protrusion Configuration Switching in Piscine Betanodavirus Implies a Novel Antiviral Strategy.
Journal, issue, pages	ACS Infect Dis, Year 2024
Publish date	Aug 1, 2024
Authors	Petra Štěrbová / Chun-Hsiung Wang / Kathleen J D Carillo / Yuan-Chao Lou / Takayuki Kato / Keiichi Namba / Der-Lii M Tzou / Wei-Hau Chang /
PubMed Abstract	Many viruses contain surface spikes or protrusions that are essential for virus entry. These surface structures can thereby be targeted by antiviral drugs to treat viral infections. Nervous necrosis ...Many viruses contain surface spikes or protrusions that are essential for virus entry. These surface structures can thereby be targeted by antiviral drugs to treat viral infections. Nervous necrosis virus (NNV), a simple nonenveloped virus in the genus of betanodavirus, infects fish and damages aquaculture worldwide. NNV has 60 conspicuous surface protrusions, each comprising three protrusion domains (P-domain) of its capsid protein. NNV uses protrusions to bind to common receptors of sialic acids on the host cell surface to initiate its entry via the endocytic pathway. However, structural alterations of NNV in response to acidic conditions encountered during this pathway remain unknown, while detailed interactions of protrusions with receptors are unclear. Here, we used cryo-EM to discover that Grouper NNV protrusions undergo low-pH-induced compaction and resting. NMR and molecular dynamics (MD) simulations were employed to probe the atomic details. A solution structure of the P-domain at pH 7.0 revealed a long flexible loop (amino acids 311-330) and a pocket outlined by this loop. Molecular docking analysis showed that the N-terminal moiety of sialic acid inserted into this pocket to interact with conserved residues inside. MD simulations demonstrated that part of this loop converted to a β-strand under acidic conditions, allowing for P-domain trimerization and compaction. Additionally, a low-pH-favored conformation is attained for the linker connecting the P-domain to the NNV shell, conferring resting protrusions. Our findings uncover novel pH-dependent conformational switching mechanisms underlying NNV protrusion dynamics potentially utilized for facilitating NNV entry, providing new structural insights into complex NNV-host interactions with the identification of putative druggable hotspots on the protrusion.
External links	ACS Infect Dis / PubMed:39087906
Methods	EM (single particle)
Resolution	2.82 - 4.36 Å
Structure data	39212 EMDB entry, No image 8yf6 EMDB-39212, PDB-8yf6: Cryo-EM structure of Dragon Grouper nervous necrosis virus-like particle at pH8.0 (3.23A) Method: EM (single particle) / Resolution: 3.23 Å 39213 EMDB entry, No image 8yf7 EMDB-39213, PDB-8yf7: Cryo-EM structure of Dragon Grouper nervous necrosis virus-like particle at pH6.5 (2.82A) Method: EM (single particle) / Resolution: 2.82 Å 39214 EMDB entry, No image 8yf8 EMDB-39214, PDB-8yf8: Cryo-EM structure of Dragon Grouper nervous necrosis virus-like particle at pH5.0 (3.52A) Method: EM (single particle) / Resolution: 3.52 Å 39215 EMDB entry, No image 8yf9 EMDB-39215, PDB-8yf9: Cryo-EM structure of Dragon Grouper nervous necrosis virion at pH6.5 (3.12A) Method: EM (single particle) / Resolution: 3.12 Å EMDB entry, No image EMDB-39217: Cryo-EM structure of Dragon Grouper nervous necrosis virion at pH5.0 (4.36A) Method: EM (single particle) / Resolution: 4.36 Å
Chemicals	ChemComp-CA: Unknown entry
Source	dragon grouper nervous necrosis virus Channa striata (snakehead murrel)
Keywords	VIRUS / nervous necrosis virus / Dragon Grouper / Cryo-EM structure